LAMMPS (3 Nov 2022)
# electrodes with constant potential and smart neighborlists
# for graphene-ionic liquid supercapacitor

boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
processors * * 2

atom_style full
pair_style lj/cut/coul/long 16
bond_style harmonic
angle_style harmonic
kspace_style pppm/electrode 1e-7
# kspace_modify in main script because ffield is periodic

read_data "data.graph-il"
Reading data file ...
  orthogonal box = (0 0 -68) to (32.2 34.4 68)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  3776 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  640 bonds
  reading angles ...
  320 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.004 seconds
  read_data CPU = 0.047 seconds

# replicate 4 4 1 # test different sys sizes

variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top
group bot subtract ele top
416 atoms in group bot

group bmi type 1 2 3
960 atoms in group bmi
group electrolyte type 1 2 3 4
1280 atoms in group electrolyte

fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
       0 = # of size 2 clusters
       0 = # of size 3 clusters
       0 = # of size 4 clusters
     320 = # of frozen angles
  find clusters CPU = 0.005 seconds

variable q atom q
compute qtop top reduce sum v_q
compute qbot bot reduce sum v_q
compute ctemp electrolyte temp
kspace_modify slab 3.0

fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on
832 atoms in group conp_group

thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
run 500

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- kspace_style pppm/electrode command:

@article{Ahrens2021,
author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0063381},
title = {{Constant potential simulations on a mesh}},
journal = {Journal of Chemical Physics},
year = {2021}
volume = {155},
pages = {104104},
}
- fix electrode command:

@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM/electrode initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.20904498
  grid = 32 32 200
  stencil order = 5
  estimated absolute RMS force accuracy = 3.7023506e-05
  estimated relative force accuracy = 1.1149519e-07
  using double precision MKL FFT
  3d grid and FFT values/proc = 151593 85504
Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 18
  ghost atom cutoff = 18
  binsize = 9, bins = 4 4 16
  3 neighbor lists, perpetual/occasional/extra = 2 1 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix electrode/conp, occasional, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) fix electrode/conp, perpetual, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
   Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop    
         0   0              0              25137190       25137190       0.0085142912  -0.0085142912 
        50   17.83755       64.26354       25137031       25137214       0.0045923944  -0.0045923944 
       100   48.393682      174.34846      25136775       25137273      -0.009514517    0.009514517  
       150   70.421272      253.7075       25136657       25137382      -0.033017005    0.033017005  
       200   82.204844      296.16031      25136670       25137517      -0.063668175    0.063668175  
       250   87.54223       315.38937      25136762       25137663      -0.096776257    0.096776257  
       300   91.704746      330.38571      25136871       25137816      -0.1283784      0.1283784    
       350   100.36017      361.56871      25136942       25137975      -0.15649799     0.15649799   
       400   111.37575      401.25467      25136994       25138141      -0.18065435     0.18065435   
       450   121.79848      438.80476      25137052       25138307      -0.19979365     0.19979365   
       500   126.95916      457.39718      25137155       25138463      -0.21037535     0.21037535   
Loop time of 48.4075 on 4 procs for 500 steps with 3776 atoms

Performance: 0.892 ns/day, 26.893 hours/ns, 10.329 timesteps/s, 39.002 katom-step/s
75.3% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.3095     | 5.5504     | 5.7923     |   8.2 | 11.47
Bond    | 0.0011128  | 0.0012414  | 0.0014028  |   0.3 |  0.00
Kspace  | 24.084     | 24.322     | 24.559     |   3.9 | 50.24
Neigh   | 0.093557   | 0.09408    | 0.094377   |   0.1 |  0.19
Comm    | 0.30394    | 0.31319    | 0.3225     |   1.6 |  0.65
Output  | 0.0012719  | 0.0015908  | 0.0024592  |   1.3 |  0.00
Modify  | 18.066     | 18.079     | 18.091     |   0.2 | 37.35
Other   |            | 0.04692    |            |       |  0.10

Nlocal:            944 ave         951 max         941 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost:        5923.25 ave        5941 max        5906 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs:         431582 ave      442090 max      419903 min
Histogram: 1 1 0 0 0 0 0 0 0 2

Total # of neighbors = 1726328
Ave neighs/atom = 457.18432
Ave special neighs/atom = 0.50847458
Neighbor list builds = 7
Dangerous builds = 0
Total wall time: 0:00:54
